[2023-03-16 23:35:13,189] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:13,189] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:13,189] [INFO] DQC Reference Directory: /var/lib/cwl/stg717ba498-6472-41bd-a9dc-2b3d6c7270ac/dqc_reference
[2023-03-16 23:35:14,952] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:14,952] [INFO] Task started: Prodigal
[2023-03-16 23:35:14,952] [INFO] Running command: cat /var/lib/cwl/stgc49f160f-7431-4ba5-a8c2-20f0c7660296/OceanDNA-b22383.fa | prodigal -d OceanDNA-b22383/cds.fna -a OceanDNA-b22383/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:56,394] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:56,394] [INFO] Task started: HMMsearch
[2023-03-16 23:35:56,394] [INFO] Running command: hmmsearch --tblout OceanDNA-b22383/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg717ba498-6472-41bd-a9dc-2b3d6c7270ac/dqc_reference/reference_markers.hmm OceanDNA-b22383/protein.faa > /dev/null
[2023-03-16 23:35:56,645] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:56,646] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc49f160f-7431-4ba5-a8c2-20f0c7660296/OceanDNA-b22383.fa]
[2023-03-16 23:35:56,680] [INFO] Query marker FASTA was written to OceanDNA-b22383/markers.fasta
[2023-03-16 23:35:56,681] [INFO] Task started: Blastn
[2023-03-16 23:35:56,681] [INFO] Running command: blastn -query OceanDNA-b22383/markers.fasta -db /var/lib/cwl/stg717ba498-6472-41bd-a9dc-2b3d6c7270ac/dqc_reference/reference_markers.fasta -out OceanDNA-b22383/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:57,188] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:57,189] [INFO] Selected 16 target genomes.
[2023-03-16 23:35:57,189] [INFO] Target genome list was writen to OceanDNA-b22383/target_genomes.txt
[2023-03-16 23:35:57,198] [INFO] Task started: fastANI
[2023-03-16 23:35:57,198] [INFO] Running command: fastANI --query /var/lib/cwl/stgc49f160f-7431-4ba5-a8c2-20f0c7660296/OceanDNA-b22383.fa --refList OceanDNA-b22383/target_genomes.txt --output OceanDNA-b22383/fastani_result.tsv --threads 1
[2023-03-16 23:36:12,715] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:12,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg717ba498-6472-41bd-a9dc-2b3d6c7270ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:36:12,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg717ba498-6472-41bd-a9dc-2b3d6c7270ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:36:12,723] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:36:12,723] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:36:12,723] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Rhodopirellula rubra	strain=CECT 8075	GCA_014192335.1	980271	980271	type	True	77.973	130	2093	95	below_threshold
Rubripirellula lacrimiformis	strain=K22.7	GCA_007741535.1	1930273	1930273	type	True	76.967	198	2093	95	below_threshold
Crateriforma conspicua	strain=Mal65	GCA_007752935.1	2527996	2527996	type	True	76.856	163	2093	95	below_threshold
Rubripirellula reticaptiva	strain=Poly59	GCA_007860175.1	2528013	2528013	type	True	76.8023	157	2093	95	below_threshold
Rubripirellula obstinata	strain=CECT 8602	GCA_001642955.1	406547	406547	type	True	76.6329	142	2093	95	below_threshold
Stieleria neptunia	strain=Enr13	GCA_007754155.1	2527979	2527979	type	True	76.4689	193	2093	95	below_threshold
Rhodopirellula islandica	strain=K833	GCA_001027925.1	595434	595434	type	True	76.4287	127	2093	95	below_threshold
Stieleria maiorica	strain=Mal15	GCA_008035925.1	2795974	2795974	type	True	76.3357	198	2093	95	below_threshold
Stieleria varia	strain=Pla52n	GCA_007860045.1	2528005	2528005	type	True	76.0133	140	2093	95	below_threshold
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.8447	91	2093	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:36:12,723] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22383/tc_result.tsv
[2023-03-16 23:36:12,724] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:36:12,724] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:36:12,724] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg717ba498-6472-41bd-a9dc-2b3d6c7270ac/dqc_reference/checkm_data
[2023-03-16 23:36:12,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:36:12,825] [INFO] Task started: CheckM
[2023-03-16 23:36:12,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22383/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22383/checkm_input OceanDNA-b22383/checkm_result
[2023-03-16 23:37:51,527] [INFO] Task succeeded: CheckM
[2023-03-16 23:37:51,528] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:37:51,531] [INFO] ===== Completeness check finished =====
[2023-03-16 23:37:51,531] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:37:51,531] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22383/markers.fasta)
[2023-03-16 23:37:51,532] [INFO] Task started: Blastn
[2023-03-16 23:37:51,532] [INFO] Running command: blastn -query OceanDNA-b22383/markers.fasta -db /var/lib/cwl/stg717ba498-6472-41bd-a9dc-2b3d6c7270ac/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22383/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:37:52,219] [INFO] Task succeeded: Blastn
[2023-03-16 23:37:52,220] [INFO] Selected 15 target genomes.
[2023-03-16 23:37:52,220] [INFO] Target genome list was writen to OceanDNA-b22383/target_genomes_gtdb.txt
[2023-03-16 23:37:52,619] [INFO] Task started: fastANI
[2023-03-16 23:37:52,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgc49f160f-7431-4ba5-a8c2-20f0c7660296/OceanDNA-b22383.fa --refList OceanDNA-b22383/target_genomes_gtdb.txt --output OceanDNA-b22383/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:38:11,308] [INFO] Task succeeded: fastANI
[2023-03-16 23:38:11,316] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:38:11,316] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_007753675.1	s__Stieleria sp007753675	78.1796	222	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741555.1	s__K23-9 sp007741555	77.2247	160	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__K23-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859915.1	s__Rhodopirellula pilleata	77.105	135	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007741535.1	s__Rubripirellula sp007741535	76.954	199	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007752935.1	s__Crateriforma conspicua	76.856	163	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Crateriforma	95.0	98.96	98.96	0.93	0.93	2	-
GCF_007860175.1	s__Rubripirellula reticaptiva	76.8023	157	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rubripirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014154935.1	s__Stieleria sp014154935	76.7671	205	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065135.1	s__Roseimaritima ulvae	76.4998	126	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	99.98	99.98	1.00	1.00	2	-
GCF_007754155.1	s__Stieleria neptunia	76.4689	193	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001027925.1	s__Rhodopirellula islandica	76.4287	127	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Rhodopirellula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008035925.1	s__Stieleria maiorica	76.3314	197	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289565.1	s__Stieleria sp002289565	76.3068	192	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007860045.1	s__Stieleria varia	76.0133	140	2093	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Stieleria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:38:11,317] [INFO] GTDB search result was written to OceanDNA-b22383/result_gtdb.tsv
[2023-03-16 23:38:11,317] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:38:11,318] [INFO] DFAST_QC result json was written to OceanDNA-b22383/dqc_result.json
[2023-03-16 23:38:11,318] [INFO] DFAST_QC completed!
[2023-03-16 23:38:11,318] [INFO] Total running time: 0h2m58s